Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

摘要: Several codon-based methods are available for detecting adaptive evolution in protein-coding sequences, but to date none specifically identify sites that selected differentially two populations, although such comparisons between populations have been historically useful identifying the action of natural selection. We developed fixed effects maximum likelihood methods: one codon positions showing selection patterns persist a population and another whether is operating on individual codons gene sampled from different populations. Applying these HIV infecting genetically distinct human hosts, we found few positively amino acid population; other changes detected only at tips phylogenetic tree appear deleterious long term. Additionally, identified seven protease reverse transcriptase samples, demonstrating specific population-level adaptation